Summary: Identification and Measurement of Neighbor Dependent
Nucleotide Substitution Processes
Peter F. Arndt
Department of Computational Molecular Biology
Max Planck Institute for Molecular Genetics
Ihnestr. 73
14195 Berlin, Germany
arndt@molgen.mpg.de
Abstract: The presence of different neighbor dependent substitution processes gener-
ates specific patterns of dinucleotide frequencies in all organisms. Based on a general
framework of how to include such processes into more realistic models of nucleotide
substitutions we develop a method that is able to identify such processes, measure their
strength, and judge their importance to be included into the modeling. Starting from a
model for neighbor independent nucleotide substitution we successively add neighbor
dependent substitution processes in the order of their ability to increase the likelihood
of the model describing the data. The analysis of neighbor dependent nucleotide sub-
stitutions in human, zebrafish and fruit fly is presented.
1 Introduction
The identity of the neighboring nucleotide can have a drastic influence on the mutation
rates of a nucleotide. A well-known and studied example of this fact is the increased